When I open network manager and import the VPN settings from the premade config folder everything takes. The problem is when I try to save the settings, the save button at the bottom of the network manager applet is greyed out. Further more when I hover over the button it says Authenticate to save this connection for all users of this machine. The problem is I did not check the box Available to all users it was already checked and it is also greyed out and won't let me manipulate it.

I had this problem too, I don't know if I could reproduce it but what I did to get round it was to change the VPN type from certificates(TLS) to password with certificates, then put in some junk text into the two password fields and fiddled with the dropdown for saving the passwords, it then let me save the connection and did store those passwords, that seemed to get it over the problem of not saving the password so I then set it back to certificates(TLS) and put in the real private key password and saved the connection and it worked. This was in a 12.04 virtualbox VM.